https://github.com/hermanzhaozzzz/bioat

bioat, a python package & command line toolkit for Bioinformatics and data science!
https://github.com/hermanzhaozzzz/bioat

bioinformatics bioinformatics-tool data-science python

Last synced: 3 months ago
JSON representation

bioat, a python package & command line toolkit for Bioinformatics and data science!

• Host: GitHub
• URL: https://github.com/hermanzhaozzzz/bioat
• Owner: hermanzhaozzzz
• License: apache-2.0
• Created: 2021-08-12T05:32:13.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2025-11-07T10:38:15.000Z (8 months ago)
• Last Synced: 2025-12-16T02:22:57.404Z (7 months ago)
• Topics: bioinformatics, bioinformatics-tool, data-science, python
• Language: Python
• Homepage: https://github.com/hermanzhaozzzz/bioat
• Size: 126 MB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# BioAT

the Bioinformatic Analysis Tools

## About bioat

Bref:  **bioat**, a python **package** & **command line toolkit** for Bioinformatics and data science!

Home: https://github.com/hermanzhaozzzz/bioat

License: Apache-2.0

| Name | Downloads | Version | Platforms | Test |

| --- | --- | --- | --- | --- |

|[![Conda Recipe](https://img.shields.io/badge/recipe-bioat-green.svg)](https://anaconda.org/conda-forge/bioat) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/bioat.svg)](https://anaconda.org/conda-forge/bioat) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/bioat.svg)](https://anaconda.org/conda-forge/bioat) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/bioat.svg)](https://anaconda.org/conda-forge/bioat) | [![Azure Pipelines](https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/bioat-feedstock?branchName=main)](https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=23719&branchName=main) |

## About author

Name: [赵华男 | Huanan Herman Zhao](https://scholar.google.com/citations?user=ojSVoWQAAAAJ&hl=en) |  EMail: hermanzhaozzzz AT gmail.com | [Zhihu](https://www.zhihu.com/people/hymanzhaozzzz) | [BLOG](http://zhaohuanan.cc)

## Installation

```shell

# supported platform: Linux / MacOS (intel & arm64) / Windows

pip install --upgrade bioat

# use conda

conda install -c conda-forge bioat

```

## Usage

```shell

# list commands

bioat list

# check version

bioat version

# check information about bioat

bioat about

# example usage

bioat bam remove_clip --help

samtools view -h test_sorted_n.bam | bioat bam remove_clip | tail

```

[circos plot](docs/demo_circos-plot.ipynb)

## Doc

See [Doc](https://bioat.readthedocs.io/en/latest/)

## Citation

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15093444.svg)](https://doi.org/10.5281/zenodo.15093444)

```latex

@software{huanan_herman_zhao_2025_15093444,

  author       = {Huanan Herman Zhao},

  title        = {BioAT, a python package \& command line toolkit for

                   bioinformatics and data science

                  },

  month        = mar,

  year         = 2025,

  publisher    = {Zenodo},

  doi          = {10.5281/zenodo.15093444},

  url          = {https://doi.org/10.5281/zenodo.15093444},

  swhid        = {swh:1:dir:19b60f4b0b93f490798727c05ab41a3222b555a1

                   ;origin=https://doi.org/10.5281/zenodo.15093443;vi

                   sit=swh:1:snp:793130e9e84df8cf427ab2b6a69c0dc77146

                   1e6a;anchor=swh:1:rel:dc0fa360dfdaf99222cf7db99e8e

                   e9e898ac1c64;path=hermanzhaozzzz-bioat-4b611f2

                  },

}

```